I see your point that once a virus gets started it can run amok, but it could still infect all the workbooks that don't already contain code, and add code to them too. In fact once a rebellious workbook is allowed to do what it wants pausing to ask about whether to enable macros in existing workbooks is going to do little to slow it down. More likely it would target other things like the registry or just delete files anyway.
I'm sure I had Excel 97 previously and opened workbooks programmatically without being asked to enable their macros, but I don't have access to it anymore so cannot be sure....
I have never seen virus protection as any more than a warning when I open new workbooks I have received, and for this it serves as a useful protection. If I am emailed a spreadsheet from an unknown source I would open with macros disabled first and check it over to make sure it won't do anything untoward. If the VBA code is protected I would not proceed unless I trusted the source.